Import Existing DNA Files to Benchling

After clicking, New DNA Sequence, click the Convert Files tab to drag and drop your existing DNA files to Benchling. In addition to GenBank and FASTA file formats, Benchling supports file types from common DNA editors, such as ApE, DNASTAR Lasergene, Geneious, Vector NTI, MacVector, SnapGene, and Serial Cloner. You can view all file formats supported by Benchling here.

Import from external databases

After clicking, New DNA Sequence, click the Search External Databases tab. You can directly import DNA sequences by typing gene name, NCBI accession number, or ENSEMBL ID. Once you type in the name of the gene, you can then select the desired genome and transcript annotation.

Customize sequence view

Split Workspace

Toggle Split Workspace at the bottom of the screen to view the DNA sequence and its map at the same time.

Arrange tabs

Drag tabs to rearrange their order.

Customize display

Click the gear icon on Sequence Map, Linear Map, or Plasmid Map to customize what the map displays.

View and create annotations

Click the Annotations button in the right sidebar to view all annotations.

To create new annotations, click New Annotation, highlight the sequence of interest, give it a name, and click Save Annotation. There is a more detailed tutorial in this article.

You can also import feature libraries and perform auto annotation. Learn how to do it in this article.

Find restriction enzyme cut sites

Click the Digests button in the right sidebar to search for restriction enzyme digestion sites.

Enter 1 under Find Enzyme to find all single cutters (learn more ways to find cut sites here). Select enzymes of interest to view them on Sequence Map. Click Run Digest to simulate a virtual digest.

Align sequences

Design CRISPR guides

Click on the CRISPR button to design guide RNAs or view existing guide analyses. We typically recommend you starting from scratch to ensure all settings are correct. View our tutorial or the blog post series to start your design.

Search DNA sequence

To search for a particular sequence, use Ctrl + F in Windows or Command + F in Mac to open a search window. Click on the gear icon for additional options, such as searching for amino acid sequences or allowing mismatches.